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- PDB-8qyu: Beta-cardiac myosin S1 fragment in the pre-powerstroke state comp... -

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Basic information

Entry
Database: PDB / ID: 8qyu
TitleBeta-cardiac myosin S1 fragment in the pre-powerstroke state complexed to Omecamtiv mecarbil
Components
  • Myosin light chain 3
  • Myosin-7
KeywordsCONTRACTILE PROTEIN / cardiac myosin modulators inherited cardiomyopathies Omecamtiv mecarbil
Function / homology
Function and homology information


muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding ...muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-2OW / ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / MALONIC ACID / VANADATE ION / Myosin light chain 3 / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRobert-Paganin, J. / Kikuti, C. / Auguin, D. / Rety, S. / David, A. / Houdusse, A.
Funding support France, United States, 4items
OrganizationGrant numberCountry
The French Muscular Dystrophy Telethon (AFM-Telethon)21805 France
Fondation pour la Recherche Medicale (FRM)DCM20181039553 France
Agence Nationale de la Recherche (ANR)21-CE11-0022-01 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1GM131981-01 United States
CitationJournal: Biorxiv / Year: 2023
Title: Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite antagonistic effects in heart contraction.
Authors: Auguin, D. / Robert-Paganin, J. / Rety, S. / Kikuti, C. / David, A. / Theumer, G. / Schmidt, A.W. / Knolker, H.J. / Houdusse, A.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-7
B: Myosin-7
G: Myosin light chain 3
H: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,99722
Polymers229,3224
Non-polymers2,67518
Water13,854769
1
A: Myosin-7
H: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,90910
Polymers114,6612
Non-polymers1,2488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-7
G: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,08712
Polymers114,6612
Non-polymers1,42610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.996, 122.503, 187.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABGH

#1: Protein Myosin-7 /


Mass: 92693.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39
#2: Protein Myosin light chain 3 /


Mass: 21968.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P85100

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Non-polymers , 9 types, 787 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical ChemComp-2OW / methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate / omecamtiv mercarbil / Omecamtiv mecarbil


Mass: 401.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2mM MgADP 5 mM Omecamtiv mecarbil 2mM vanadate 24% PEG 3350 5% Tacsimate pH 6.0 5mM TCEP 20% Glycerol 10% DMSO DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.928→102.547 Å / Num. obs: 97819 / % possible obs: 93.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.153 / Net I/σ(I): 7.9
Reflection shellResolution: 1.928→2.128 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.267 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4891 / CC1/2: 0.519 / % possible all: 73.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→22.63 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4645 5.02 %RANDOM
Rwork0.191 ---
obs0.194 92500 57.2 %-
Displacement parametersBiso mean: 38.61 Å2
Baniso -1Baniso -2Baniso -3
1-10.3159 Å20 Å20 Å2
2---7.036 Å20 Å2
3----3.2799 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.96→22.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14596 0 216 769 15581
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115156HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.120414HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5479SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes417HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2199HARMONIC5
X-RAY DIFFRACTIONt_it15156HARMONIC5
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion18.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1940SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17510SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 -4.91 %
Rwork0.227 271 -
all0.229 285 -
obs--2.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42280.2652-0.14980.4091-0.17890.40630.0474-0.0370.04010.0254-0.0152-0.0375-0.0305-0.0674-0.03220.0744-0.0040.0062-0.1404-0.0075-0.1063-5.7893-6.041341.5175
20.52130.1511-0.04150.7212-0.05460.26690.02540.03960.0263-0.0061-0.04360.03430.0186-0.02220.01820.0677-0.0032-0.0086-0.16610.0127-0.127-33.4424-19.937216.7988
33.96593.2415-0.08628.4316-0.6681.41260.00930.0843-0.3285-0.0108-0.2324-0.40.0480.0920.2231-0.1001-0.01470.0161-0.32860.07-0.1161-33.5257-72.401231.5968
40.58430.6806-0.18381.7097-0.2551.0015-0.0009-0.02380.0818-0.1242-0.01620.21410.0703-0.14140.01710.15380.0091-0.0144-0.1790.049-0.116315.530930.55816.6271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ G|* }
4X-RAY DIFFRACTION4{ H|* }

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